Anatomy: FEM mesh generation with SimNIBS4/CHARM

doc/updates.txt

@@ -1,11 +1,13 @@
 February 2023
 - Stat: Added FieldTrip threshold-free cluster enhancement (TFCE)
 - Anatomy: Compute FEM mesh statistics
+- Anatomy: FEM mesh generation with SimNIBS4/CHARM
+- Anatomy: Fixes in template ICBM152 2023 (T1 contrast & tissue labels)
 - Bugfix: Error in data covariance computation: Baseline not removed
 | when baseline time window was not included in data time window
 --------------------------------------------------------------
 January 2023
-- Anatomy: New template ICBM152 2022
+- Anatomy: New template ICBM152 2023
 - Anatomy: Remove selection of fiducials when setting anatomy template
 - Anatomy: Project scouts between hemispheres using the anatomy template
 - Distrib: Enable compilation on Linux and MacOS

toolbox/anatomy/mri_getlabels.m

@@ -57,17 +57,23 @@
 if (any(MriFile == '.') || (length(MriFile) > maxNameLength)) && file_exist(MriFile)
     % Get file name
     [fPath, fBase, fExt] = bst_fileparts(MriFile);
-    % LABELS: Try to get a side .txt with the labels
+    % LABELS MRIcron: Try to get a side .txt with the labels
     LabelsFile = bst_fullfile(fPath, [fBase, '.txt']);
     if file_exist(LabelsFile)
         Labels = in_label_mricron(LabelsFile);
     end
     fBase = strrep(fBase, '.nii', '');
-    % LABELS: Try to get a side .csv with the labels
+    % LABELS CAT12: Try to get a side .csv with the labels
     LabelsFile = bst_fullfile(fPath, [fBase, '.csv']);
     if file_exist(LabelsFile)
         Labels = in_label_cat12(LabelsFile);
     end
+    % LABELS SimNIBS4: Try to get a side _LUT.txt with the labels
+    LabelsFile = bst_fullfile(fPath, [fBase, '_LUT.txt']);
+    if file_exist(LabelsFile)
+        Labels = in_label_simnibs(LabelsFile);
+    end
+
     % If labels were read: use the filename as the atlas name
     fBase = lower(fBase);
     if ~isempty(Labels)
@@ -77,7 +83,7 @@
         AtlasName = 'freesurfer';
     elseif ~isempty(strfind(fBase, '.svreg.label'))   % *.svreg.label.nii.gz
         AtlasName = 'svreg';
-    elseif ~isempty(strfind(fBase, '_final_contr'))
+    elseif ~isempty(strfind(fBase, '_final_contr')) || ~isempty(strfind(fBase, 'final_tissues'))  % SimNIBS3/headreco  &  SimnNIBS4/charm
         AtlasName = 'simnibs';
     end
 end
@@ -118,13 +124,19 @@
                     5, 'Scalp',         [255, 205, 184]};
         case 'simnibs'
             Labels = {...
-                    0, 'Background',    [  0,   0,   0]; ...
-                    1, 'White',         [220, 220, 220]; ...
-                    2, 'Gray',          [130, 130, 130]; ...
-                    3, 'CSF',           [ 44, 152, 254]; ...
-                    4, 'Skull',         [255, 255, 255]; ...
-                    5, 'Scalp',         [255, 205, 184]; ...
-                    6, 'Eyes',          [255,   0, 255]};
+                    0,   'Background',    [  0,   0,   0]; ...
+                    1,   'White',         [220, 220, 220]; ...
+                    2,   'Gray',          [130, 130, 130]; ...
+                    3,   'CSF',           [ 44, 152, 254]; ...
+                    4,   'Skull',         [255, 255, 255]; ...
+                    5,   'Scalp',         [255, 205, 184]; ...
+                    6,   'Eyes',          [255,   0, 255]; ...
+                    7,   'Compact_bone',  [255, 239, 179]; ...
+                    8,   'Spongy_bone',   [255, 138,  57]; ...
+                    9,   'Blood',         [  0,  65, 142]; ...
+                    10,  'Muscle',        [  0, 118,  14]; ...
+                    100, 'Electrode',     [  37, 79, 255]; ...
+                    500, 'Saline_or_gel', [103, 255, 226]};
     end
 end
 

toolbox/core/bst_get.m

@@ -3466,7 +3466,8 @@
                     {'.gii'},   'GIfTI / World coordinates (*.gii)', 'GII-WORLD'; ...
                     {'.fif'},   'MNE (*.fif)',             'FIF'; ...
                     {'.obj'},   'MNI OBJ (*.obj)',         'MNIOBJ'; ...
-                    {'.msh'},   'SimNIBS Gmsh4 (*.msh)',   'SIMNIBS'; ...
+                    {'.msh'},   'SimNIBS3/headreco Gmsh4 (*.msh)', 'SIMNIBS3'; ...
+                    {'.msh'},   'SimNIBS4/charm Gmsh4 (*.msh)', 'SIMNIBS4'; ...
                     {'.tri'},   'TRI (*.tri)',             'TRI'; ...
                     {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz', '_subjectimage'}, 'Volume mask or atlas (subject space)', 'MRI-MASK'; ...
                     {'.mri', '.fif', '.img', '.ima', '.nii', '.mgh', '.mgz', '.mnc', '.mni', '.gz'},                  'Volume mask or atlas (MNI space)',     'MRI-MASK-MNI'; ...

toolbox/gui/view_surface_fem.m

@@ -151,7 +151,7 @@
 % Transparency and color
 if (size(SurfColor,2) ~= Ntissue)
     ColorOrder = panel_scout('GetScoutsColorTable');
-    SurfColor = ColorOrder(1:Ntissue, :);
+    SurfColor = ColorOrder(mod((1:Ntissue)-1, length(ColorOrder)) + 1, :);
     labels = lower(FemMat.TissueLabels);
     % Get default color for each layer
     for iTissue = 1:Ntissue
@@ -181,6 +181,7 @@
     Resect = [0, 0.01, 0];
 end
 % Plot each tissue as a patch object
+iTess = 0;
 for iTissue = 1:Ntissue
     % Progress bar
     MeshName = [SurfaceFile, '(', FemMat.TissueLabels{iTissue}, ')'];
@@ -190,6 +191,9 @@
     end
     % Select elements of this tissue
     Elements = FemMat.Elements(FemMat.Tissue == iTissue, 1:4);
+    if isempty(Elements)
+        continue;
+    end
     % Create a surface for the outside surface of this tissue
     Faces = tess_voledge(FemMat.Vertices, Elements, Resect);
     % Plot as a new surface
@@ -203,7 +207,8 @@
                 'SpecularExponent', 0.3, ...
                 'UserData',         Elements);
     % Show edges
-    panel_surface('SetSurfaceEdges', hFig, iTissue, 1);
+    iTess = iTess + 1;
+    panel_surface('SetSurfaceEdges', hFig, iTess, 1);
 end
 if isProgress
     bst_progress('text', 'Creating figure...');

toolbox/io/import_anatomy_fs.m

@@ -481,7 +481,7 @@
     oldCortexLowFile = file_fullpath(CortexLowFile);
     CortexLowFile    = bst_fullfile(bst_fileparts(oldCortexLowFile), 'tess_cortex_pial_low.mat');
     file_move(oldCortexLowFile, CortexLowFile);
-    CortexHiFile = file_short(CortexHiFile);
+    CortexLowFile = file_short(CortexLowFile);
 else
     CortexHiFile = [];
     CortexLowFile = [];